Variant report

Variant	rs12280342
Chromosome Location	chr11:15875139-15875140
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10766285	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832524	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10832525	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11023742	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11023747	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11023753	0.90[CEU][hapmap];0.90[JPT][hapmap]
rs11023754	0.82[CEU][hapmap]
rs11023757	0.85[AFR][1000 genomes]
rs12270494	0.80[AFR][1000 genomes]
rs12289250	0.85[AFR][1000 genomes]
rs12290232	0.89[AFR][1000 genomes]
rs12364139	0.85[CEU][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap]
rs12797447	0.82[AMR][1000 genomes]
rs1440707	0.85[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap]
rs2119376	0.89[AFR][1000 genomes]
rs4756833	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757370	0.85[AFR][1000 genomes]
rs4757371	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs4757373	0.85[CEU][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832073	chr11:15822409-15984078	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12280342	DKK3	cis	cerebellum	SCAN
rs12280342	FAR1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:15866800-15877800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:15873400-15882800	Weak transcription	Right Atrium	heart
3	chr11:15873800-15875200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr11:15875000-15876600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr11:15875000-15880000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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